Thursday, September 13, 2012

James Shapiro Claims Credit for Predicting That Junk DNA Is Actually Part of a "highly sophisticated information storage organelle"

Do you remember James Shaprio? He's the University of Chicago scientist who claims to have discovered a new theory of evolution in his book evolution: A View from the 21st Century [see my review in NCSE Reports]. The book criticizes the old hardened version of the Modern Synthesis and never mentions things like random genetic drift or Nearly-Neutral Theory. It's difficult to imagine how someone could criticize evolutionary theory without understanding population genetics but he managed to pull it off.

You might also recall that he's the scientist who criticized the Central Dogma of Molecular Biology when he clearly didn't understand it [Revisiting the Central Dogma in the 21st Century]. I was shocked to learn that he had published a paper with the title "Revisiting the Central Dogma in the 21st Century" without ever bothering to read the literature to find out how Francis Crick actually defined the Central Dogma. (In fact, Shapiro misrepresented Crick's view.) It goes to show you how silly you look when you criticize something you don't understand.

Shapiro continues by mentioning the ENCODE papers and their conclusion that 80% of our genome has a "biochemical" function. Shapiro then says,

In other words, the old idea of the genome as a string of genes interspersed with unimportant noncoding DNA is no longer tenable. Many eminent scientists had opined that the noncoding DNA, much of it repeated at many different locations, is nothing more than "junk DNA." ENCODE revealed that most (and probably just about all) of this noncoding and repetitive DNA contained essential regulatory information. Moreover, much of it was also copied into RNA with additional but still unknown functions.

Oh dear, two major examples of lack of understanding in the same paragraph. First, Shapiro repeats the old myth that there were "eminent scientists" who thought that all noncoding DNA was junk. Second, he takes the claim that 80% of our genome has a "biochemical function" and translates that as "ENCODE revealed that most (and probably just about all) of this noncoding and repetitive DNA contained essential regulatory information."

It's going to be difficult to take James Shapiro seriously after that, but let's try.

I had a longstanding, personal interest in the repetitive part of our genomes (up to as much as two-thirds of all our DNA) because it is composed of mobile genetic elements. I first discovered these elements in bacteria in my thesis research in 1968. I remember being scientifically offended by a 1980 article from Francis Crick and Leslie Orgel describing this DNA as "selfish" and functionless.

My interest in the roles of repetitive and mobile DNA has continued since my thesis more than four decades ago. The initial sequencing of the human genome in 2001 found over 40% to be mobile repeats spread throughout our genomes, thirty times more than protein-coding DNA.

In 2005, I published two articles on the functional importance of repetitive DNA with Rick von Sternberg. The major article was entitled "Why repetitive DNA is essential to genome function."

Shapiro is referring to the sequences that are related to transposons of various sort (LINEs and SINEs) [Junk in Your Genome: SINES ] [Junk in your Genome: LINEs]. Almost all of this is defective or inactive transposons and bits and pieces of transposons. We know from studying the evolutionary history of this DNA that very, very, few of the transposons are active.

In the paper with (von) Sternberg he also discusses highly repetitive DNA. The paper reads very much like his book. It consists of dozens of examples of specific cases in various species where little bits of repetitive DNA have been implicated in a biological function. It's the same data that Jonathan Wells uses in his book The Myth of Junk DNA.

These articles with Rick are important to me (and to this blog) for two reasons. The first is that shortly after we submitted them, Rick became a momentary celebrity of the Intelligent Design movement. Critics have taken my co-authorship with Rick as an excuse for "guilt-by-association" claims that I have some ID or Creationist agenda, an allegation with no basis in anything I have written.

Shapiro is famous for promoting a "third way" of looking at biology; a way that's not strictly Intelligent Design Creationist, but also not strictly science. He has published on the main Intelligent Design Creationist blog, Evolution News & Views and is widely quoted and admired by creationists who rightly see his views as supportive of theirs. None of that means, of course, that Shapirio is a full supporter of Intelligent Design Creationism.

The second reason the two articles with Rick are important is because they were, frankly, prescient, anticipating the recent ENCODE results. Our basic idea was that the genome is a highly sophisticated information storage organelle. Just like electronic data storage devices, the genome must be highly formatted by generic (i.e. repeated) signals that make it possible to access the stored information when and where it will be useful.

Please be careful about how you interpret this statement. On the surface it looks exactly like something the Intelligent Design Creationists would say but James Shapiro insists that he is not one of them. He has a completely different reason for thinking that our entire genome looks like a sophisticated data storage device.

Although we could not predict in detail all the ways repeated DNA would serve genome functions, I think our statements stand up well in light of the recent data. Without knowing the specifics, we were correct in asserting that the genome had to be highly formatted to serve as the marvelous information organelle it is in every living cell and organism.

So, while Rick's choice of evolutionary philosophies is different from mine, I am grateful to him for doing so much work on a paper that remains a source of justified scientific pride. Thinking of the genome informatically and of mobile DNA as a potent force for genome organization are central to the arguments presented on this blog and in my book.

We know what Rick (von) Sternberg's motives were. They weren't the same as James Shapiro's but the result is the same: bad science, lack of understanding, and flawed reasoning.

This appears to be an unusual case of someone who looks like a creationist, talks like a creationist, and hangs out with creationists, but isn't a creationist.

73 comments
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Larry, when are you going to publicly acknowledge in your writing that the terms "intelligent design" and "creationist" don't belong together in the same breath? It's like pairing the words "evolution" with "atheist". The implications of a scientific theory are not the same as the theory itself. I know. If you did stop, you'd be showing that you have a serious contender to debate - intelligent design. And so you continue to misrepresent the other side, admitting in the process that you just don't have what it takes to go head to head with ID.

Apparently Prof. Shapiro also published a paper with nutcase creationist Richard Sternberg which I mentioned in an earlier thread. That speaks very poorly of Prof. Shapiro who has a tenured faculty position at the prestigious Un. of Chicago, where he is a colleague of Jerry Coyne.

I think that Sternberg was either a postdoc or a grad student with Shapiro, if I remember correctly. I try not to fault those poor supervisors who get to be the victims of the creationist charlatans who want a degree just for the sake of having "credentials" to then propagandize against evolution. But after this one I think that Shapiro is just an idiot, and at fault. A self-serving ass-hole trying to become famous out of misleading controversy.

IDiocy is a form of creationism. No way around. It does not matter if judges have declared so or not. I have read their shit, I have talked with some of the main cdesign proponentists, and they clearly are creationists. ALl they do is recycle same-old same-old creationist propaganda. They sometimes update their "references," but the main "arguments" remain the same. Same tactics, everything. The day they do differently I might start thinking differently about them. But for as long as they just recycle, and "update," creationist propaganda with new names, they are creationists. Why deny it? Why not come out of the closet? We know they are, they know they are, why continue pretending?

"intelligent design" and "creationist" don't belong together in the same breath

Oh, come on! Do you think we forgot about Of Pandas and People and how early drafts said "creationism", and after the 1987 SCOTUS decision, they did copy and replace to change it to "Intelligent Design" without otherwise changing the definition?

Behe asserts that his Irreducible Complexity is an updated version of Paley's pocketwatch argument. Paley's book was called "Natural Theology."

Steve Fuller, the pro-ID philosopher, just said that ID proponents have an answer to "bad design" arguments: theodicy. Theodicy is a branch of theology.

Intelligent Design was always considered a branch of theology. The phrase "Intelligent Design" has been used by creationists for +140 years.

In 1874, creationist Charles Hodge used the phrase "Intelligent Design" in What Is Darwinism? (His answer: atheism.) Hodge asserted that the argument from "Intelligent Design", in just those words, is essential to Christianity, so any attack on it is an atheist attack on Christianity.

In 1923, preacher T. T. Martin used the phrase "Intelligent Design" in Hell and the High Schools.

In the early 20th century most young earth Creationists were Seventh Day Adventists, and in the 1920's the phrase "Intelligent Design" appeared in Seventh Day Adventist creationist literature.

Of course in the 1970's, the English creationist A. E. Wilder-Smith (who was the real founder of Intelligent Design jargon/"theory"), used the phrase "Intelligent Nipple Designer" (referring to a whale's nipple.)

If you don't believe in Intelligent Design, how do they react? They quote Romans 1 at you! They say that if you don't believe in Intelligent Design, you are "without excuse" and you will turn gay or lesbian (that is exactly what Romans 1 predicts.)

So in 1987, when they did copy and replace on Of Pandas and People and produced drafts with the transitional fossil "cdesign proponentsists", it was already long-established that ID was an essential part of Christian theology and if you don't agree, you're an anti-Christian atheist.

Sorry pal, we know the history of creationism a lot better than you do.

Intelligent Design was always considered a branch of theology. The phrase "Intelligent Design" has been used by creationists for +140 years.

In 1874, creationist Charles Hodge used the phrase "Intelligent Design" in What Is Darwinism? (His answer: atheism.)

Well, it's been used by Darwinists for longer than that, including old Chuck, himself.

The point which you raise on intelligent Design has perplexed me beyond measure; & has been ably discussed by Prof. Asa Gray, with whom I have had much correspondence on the subject.— I am in a complete jumble on the point. One cannot look at this Universe with all living productions & man without believing that all has been intelligently designed; yet when I look to each individual organism, I can see no evidence of this. For, I am not prepared to admit that God designed the feathers in the tail of the rock-pigeon to vary in a highly peculiar manner in order that man might select such variations & make a Fan-tail; & if this be not admitted (I know it would be admitted by many persons), then I cannot see design in the variations of structure in animals in a state of nature,—those variations which were useful to the animal being preserved & those useless or injurious being destroyed. But I ought to apologise for thus troubling you.

http://www.darwinproject.ac.uk/entry-3154

To be fair to this Hodge guy, but maybe he'd read Haeckel, who pretty much said that Darwinism did equal atheism, his materialistic monism, about six years before that, in the book that Darwin, himself, had praised and recommended, I believe four years before your Hodge date. Do you have a link to the document, I wouldn't believe a characterization of a document without being able to look at the whole thing. Not on this issue.

If you believe in a creator then you are a creationist. There are several flavors of creationists. The most important ones are Young Earth Creationists (YECs), Old Earth Creationists (OECs), Intelligent Design Creationists, and Theistic Evolution Creationists.

I think this is an example of denotative drift. As used by the great geneticist and Darwinist, T. Dobzhansky, "creationist" does have the meaning you assert here. As usually used, thought it means someone who believes in the literal truth of the creation account in Genesis. Accounts, really, as there are two included in Genesis. A "theistic evolution "creationist" (never seen it put that way) would be an evolutionist. Asa Gray would be one and if you've gone over his correspondence with Darwin, it would be hard to imagine he'd have developed his theory without Gray's extensive help and support.

The real problem only comes when someone wants to mix creationism into science, as you seem to want to accuse Shapiro of doing, perhaps with some justification, or they want to insert extrinsic content into public school classrooms. And it's not just creationists who want to do that, ideological materialism and other ideologies are far more of a danger of being successfully inserted into both.

What do you know, good old Project Gutenberg has a copy of "What is Darwinism" and it shows that Charles Hodge was aware of Haeckel's stuff.

The conclusion of the whole matter is, that the denial of design in nature is virtually the denial of God. Mr. Darwin's theory does deny all design in nature, therefore, his theory is virtually atheistical; his theory, not he himself. He believes in a Creator. But when that Creator, millions on millions of ages ago, did something,—called matter and a living germ into existence,—and then abandoned the universe to itself to be controlled by chance and necessity, without any purpose on his[Pg 174] part as to the result, or any intervention or guidance, then He is virtually consigned, so far as we are concerned, to non-existence. It has already been said that the most extreme of Mr. Darwin's admirers adopt and laud his theory, for the special reason that it banishes God from the world; that it enables them to account for design without referring it to the purpose or agency of God. This is done expressly by Büchner, Haeckel, Vogt, and Strauss. The opponents of Darwinism direct their objections principally against this element of the doctrine. This, as was stated by Rev. Dr. Peabody, was the main ground of the earnest opposition of Agassiz to the theory. America's great botanist, Dr. Asa Gray, avows himself an evolutionist; but he is not a Darwinian. Of that point we have the clearest possible proof. Mr. Darwin, after explicitly denying that the variations which have resulted in "the formation of the most perfectly adapted animals in the world, man included, were intentionally and specially guided," adds: "However much we may wish it, we can hardly follow Professor Asa Gray in his belief 'that variation has been led along certain beneficial lines' like a stream 'along definite[Pg 175] and useful lines of irrigation.'"[58] If Mr. Darwin does not agree with Dr. Gray, Dr. Gray does not agree with Mr. Darwin. It is as to the exclusion of design from the operations of nature that our American, differs from the English, naturalist. This is the vital point. The denial of final causes is the formative idea of Darwin's theory, and therefore no teleologist can be a Darwinian.

Doesn't sound like some ignorant yahoo who hadn't looked at the issue.

In his Natürlische Schöpfungsgeschichte, Haeckel is still more exclusive. When he comes to answer the objections to the evolution, or, as he commonly calls it, the descendence theory, he dismisses the objections derived from religion, as unworthy of notice, with the remark that all Glaube ist Aberglaube; all faith is superstition. The objections from a priori, or intuitive truths, are disposed of in an equally summary manner, by denying that there are any such truths, and asserting that all our knowledge is from the senses. The objection that so many distinguished naturalists reject the theory, he considers more at length. First, many have grown old in another way of thinking and cannot be expected to change. Second, many are collectors of facts, without studying their relations, or are destitute of the genius for generalization. No amount of material makes a building. Others, again, are specialists. It is not enough that a man should be versed in one department; he must be at home in all: in Botany, Zoölogy, Comparative Anatomy, Biology, Geology, and Palæontology. He must be able to survey the whole field. Fourthly, and mainly, naturalists are generally lamentably deficient in philosophical culture and in a philosophical spirit. "The immovable edifice of the true, monistic science, or what is the same thing, natural science, can only arise through the most intimate interaction and mutual interpenetration of philosophy and observation (Philosophie und Empirie)." pp. 638-641. It is only a select few, therefore, of learned and philosophical monistic materialists, who are entitled to be heard on questions of the highest moment to every individual man, and to human society.

Didn't I tell you there was nothing new in this 160 Years War and Counting?

The Thought CriminalThursday, September 13, 2012 4:13:00 PMA "theistic evolution "creationist" (never seen it put that way) would be an evolutionist.

Not at all. First, theistic evolution has been called creationism, just not often enough. Second, it should be called creationism all the time because it is.

The reason people don't understand that is the same reason people don't understand what junk DNA is - because they don't understand the nearly neutral theory of molecular evolution. I've said this before, so I will repeat myself, but it has to be said again. You have to think about what TE has to posit if it is to be consistent with both the theory of evolution and with theology.

The first non-negotiable requirement is that humans have to be the inevitable outcome of the process (you can, of course, argue that it could have been some other intelligent creature, but you move onto a really shaky theological ground if you choose to do so and what follows still applies in that case too).

The second non-negotiable (but usually neglected) requirement is that you accept the theory of evolution, which means accepting molecular evolution and population genetics, and so it happens that those have demonstrated quite convincingly that random processes have played a huge role in our evolution, and continue to do so because we're big eukaryotes with small effective population sizes .

Now, if you're a theistic evolutionist you can claim that God set things in motion and he used natural selection as a mechanism that would eventually result in the evolution of humans. But that only works if you are a pan-selectionist and modern evolutionary biology is not pan-selectionist and there are no indications it will ever be pan-selectionist again. So you are left with two choices - either God actively intervened multiple times to segregate gametes and cause specific mutations, or he has the trajectory of pretty much every single particle in the Universe predetermined from the very beginning billions of years into the future. The former is pure creationism, the latter is not only pure creationism too (just not of the YEC kind) but it also seriously messes up a lot of the elaborate theological edifice that has been built over the centuries regarding issues such as free will, etc.

So, again, TE is creationism, it is just that people don't realize it because they don't know enough about molecular evolution. The only way you can distinguish TE from creationism is if you define creationism, whether OEC or YEC as poofing living things into existence while in TE it was the universe that was created. But given that it had to lead to humans, I don't see that as a very big difference.

I'm quite sure that Dobzhansky would be surprised to find out he wasn't an evolutionist, as would Asa Gray and countless other people who had rather prominent careers in science, many of them in evolutionary science and its supporting branches. You figure Dobzhansky and Francis Collins didn't and don't know enough about molecular evolution to know that? Does your rule rule out the massively ignorant blog tread atheists, many of whom probably learned everything they know about DNA from cable TV, from being evolutionists? I would guess old Charles Darwin knew even less than that about molecular evolution. Not to mention just about the entire first forty or so years of evolutionists, until the Mendelian "rediscovery".

I know that atheists figure they've got a trademark on the universe and can vote people in and out of the Science Club but, really, you really don't have that power. That would be the preview of degree granting institutions, the editors of journals, reviewers, etc. Not to mention those who hire people to work as scientists. Luckily, not all of them are bigots of the John Maddox variety.

I could add that Charles Darwin would be surprised to find that Asa Gray wasn't an evolutionist and could produce dozens of letters to support that contention but I doubt you boys read my links so I won't go to the bother.

What a patently dishonest dodge. Especially after your last comment, which is entirely an argument from authority, your alleged authority to expel some of the most prominent names in molecular biology and in other branches of evolutionary biology. Who died and made you God?

Georgi, where are you getting this notion that evolution HAD to lead to humans from? Maybe that's what Christianity teaches, but I don't think Eastern religions teach that. They don't even seem to teach that each of us is, really, human. We are Consciousness playing out a vast array of experiences and incarnations, in what is known as 'maya'. Humans just happen to be one of those types of experiences that is able to glimpse the process, however dimly. We are not considered to be an end, not collectively; and our current existence as humans is not seen as a particularly significant event either, in the Eastern traditions. This is all just a conscious universe experiencing itself.

The question of whether or not evolution had to lead to humans is kind of moot, since humans evolved. As did every other species that lives with us, before we destroy it. But I was going to add something that another, prominent population geneticist said:

First, as others have pointed out, if he is right, the design hypothesis essentially must be wrong and the alternative naturalistic hypothesis essentially must be right. But since when is a scientific hypothesis confirmed by philosophical gymnastics, not data? Second, the fact that we as scientists find a hypothesis question-begging—as when Dawkins asks “who designed the designer?”—cannot, in itself, settle its truth value. It could, after all, be a brute fact of the universe that it derives from some transcendent mind, however question-begging this may seem. What explanations we find satisfying might say more about us than about the explanations. Why, for example, is Dawkins so untroubled by his own (large) assumption that both matter and the laws of nature can be viewed as given? Why isn’t that question-begging?

H Allen Orr: A Mission to Convert, NYRB 2007

Would his statement get him kicked off of the island, G.M? Really, your program of expulsions and exiles would be the most serious decimation of evolutionary biology since Lysenko was getting real scientists offed, really, killed in the atheist paradise. With the support of Oparin, I'll add.

We are Consciousness playing out a vast array of experiences and incarnations, in what is known as 'maya'.

No, maya is the illusion of dvaita, the distinction between consciousness and matter, or between Atman and Brahman. In Advaita Vedanta, Brahman = Atman. We are Atman, but because of Maya you don't know Atman = Brahman.

Maya also causes theism: a personal God is a projection of Brahma onto Maya, like a movie projected on a spray of water.

Wikipedia: Maya or Māyā (Sanskrit माया māyāa[›]), in Indian religions, has multiple meanings, usually quoted as "illusion", centered on the fact that we do not yet experience the environment directly but rather through some projection of it—Maya sustains the self by blessing self judgement of self creation. Māyā is the principal deity that manifests, perpetuates and governs the illusion and dream of duality in the phenomenal Universe. A mystic may attain self-realization observing the manifestations of Maya.[1] Each person, each physical object, from the perspective of eternity, is like a brief, disturbed drop of water from an unbounded ocean. The goal of enlightenment is to understand this—more precisely, to experience this: to see intuitively that the distinction between the self and the Universe is a false dichotomy. From the perspective of Maya any distinction between consciousness and physical matter, between mind and body (refer bodymind) is a kind of illusion of the unenlightened. [End wiki]

The only way you can distinguish TE from creationism is if you define creationism, whether OEC or YEC as poofing living things into existence while in TE it was the universe that was created. But given that it had to lead to humans, I don't see that as a very big difference.

I don't see why we need to lump Ken Miller in with Ken Ham. What's the point? To me, there's a big difference between Ken Ham's dinosaur with a saddle and Ken Miller snapping a cracker.

Georgi does point out some logical inconsistencies in the thought of theistic evolutionists. Sure, they're logically inconsistent, in the relationship between their theology and their understanding of convergent evolution, neutral drift, etc. But who the hell is ever completely logically consistent?

I read Ken Miller's "Only A Theory." Miller (I think it was in "Only A Theory") says evolution is not atheistic, nor random, because of convergent evolution. So the universe is fine-tuned to make some kind of intelligence. He doesn't precisely say that the universe was set up to make Homo sapiens, a primate with two arms, two legs, forward-facing eyes, etc. He just says the universe was setup to lead, by convergent evolution, to intelligence.

The whole time I was reading it I thought, "Well, then why couldn't a sapient race of elephants be produced by your God's universe? With an elephant Christ saying 'this peanut is my body'? Betrayed by pachy-Judas? Resurrected from the elephant graveyard? And Christian elephants today eating holy peanuts?"

"Or a sapient race of octopuses, produced by your God's universe? With an octo-Christ, saying 'this abalone is my body.' Betrayed by Judas wonderpus, left to dry out on the sandbar? And Christian octopi eating holy abalone?"

Sure, the logic is bollocks. We can't say intelligence is the result of convergent evolution because we've only got one example of it.

But whatever you think of TE logic, it's still not as patently dishonest as ID creationism.

You can have a fair argument with TEists. You can ask them a straight question and they will give you a straight answer. You can't have a fair argument with ID creationists-- they weasel out of everything. You can't ask them a straight question and get a straight answer. I would never accuse Ken Miller or Francis Collins of creationism.

Diogenes, I like, and appreciate, the points you are raising on this thread. I think you are expanding the field of ideas upon which these questions can be considered . From what I gather from your words, 'creationist' should not be used as a blanket term. I agree. I think the term is too closely identified with a particular type of religious believer who adheres to dogma in the face of all evidence or challenge. Everything always returns to the dogma.

Ohh clearly you are right... intelligent design has nothing whatsoever to do with the creationist movement.

Thats why creationists think its nonsense obviously yes?

Its also why they never mentioned it once in their wedge strategy, had nothing to do with the Dover thing, and why Behe has never worked for or had any involvement with creationism....

Its also why a creationist book is word for word an intelligent design book with the words 'intelligent design' replacing 'creator'

And also why advocates of 'intelligent design' are predominantly creationists.

Clearly no relationship whatsoever.... how could anyone even conceive of such a thing... It's be like labelling those who believe in UFO conspiracy theories as predominantly deluded and uneducated... ohh wait a minute.

GT: Judge Jones from the Dover case clearly stated that intelligent design is a form of creationism and cannot disentangle itself from its religious roots. If even judges can understand this, scientists should understand it even better. In fact this is precisely how ID proponents want to sneak in their religious agenda, by claiming that ID is not creationism.

Larry, by your definition of "creationist," Ken Miller would be considered a creationist. Taking him at his own word, he believes in a creator. So as you use it, "creationist" tells nothing about whether a person is entirely convinced of the truth of Darwinian evolutionary theory, partly convinced, or entirely unconvinced. In the context of a debate about evolution, the term adds little or no relevant information. Yet you use it over and over.

I think by anyone's light, when it comes to Darwinian theory, Ken Miller's perspective has nothing in common with Ken Ham's. Your stamping them both with the same label only confuses and misleads. So why not just drop it? Communication entails making distinctions. Language is supposed to clarify not cloud.

"If you are entirely convinced of the truth of evolution then you can't be a creationist."

Yes, you can. Evolution describes a process that is taking place on perhaps only one planet in a universe containing trillions of stars. It has been going on for perhaps 3 billion years on this one small planet in a vast universe that is estimated to be something like 16 billion years old. So it is very possible to be a 'creationist', and believe that the universe was birthed through some sort of conscious/creative process, while still acknowledging evolution takes place on a rock in space. Evolution doesn't touch on the origin of the universe. Currently, it doesn't even touch on the origin of life, other than theorize that the processes leading up to the emergence of the first self replicating cell were almost certain the same basic processes that governed their course after they came into being.

You can even believe in The Gaia Hypothesis and accept that evolution is playing out within that larger concept of an ordered, self regulating planet.

If you want to be picky then it's possible to accept all the facts and implications of evolution and still be a Deist. Problem is, there aren't any Deists.

All other creationists posit events than conflict with what we know about evolution. That's why people like Ken Miller and Francis Collins have to write books explaining (unsuccessfully) how they rationalize their beliefs with science.

It's not a matter of being picky, it's about rounding up words and making sure people can agree on what they mean. When you wrote 'the truth of evolution' you were more accurately referring to the implications of evolution. But evolution can imply different things to different people. For example, Jim Shapiro. You can't call him a deist, because he hasn't stated that he is one, and he has unambiguously denied that he is an ID proponent. He doesn't appear to be a Christian or a member of another orthodox, organized religion. He does seem rather firmly convinced that something as yet not understood is driving evolution. Currently accepted explanations don't satisfy him.That indicates to YOU that he is a ipso facto creationist. But what matters is what HE thinks, not whatever cubicle you want to rope him into based upon your inferences.

All other creationists posit events than conflict with what we know about evolution.

All other?

Since you are obviously extending the current use of the term "creationist" to mean anyone who believes in God, you are talking about billions of people. Your ability to know what all of them "posit" is something any rational consideration would call into question. And there are things you "know" about evolution that I'd suspect would more accurately be considered to be beliefs, such as that all of what you include as "junk" DNA is actually non-functioning.

There are plenty of things that atheists believe that conflicts with what is known about evolution. You and Dawkins can't both be right about evo-psy. Gould and Dennett can't both be right about spandrels. As it happens, I'm closer to your side than Dawkins and Dennett on those issues. Though the more I read about evolutionary science the more impressed I am in how much of metaphor there is in the assertions of science and how its main theory, natural selection, is less a theory than it is a habit of thinking about an enormous range of very different events and conditions.

It is quite possible to believe that whatever science can correctly say about evolution is true and that is part of how God creates the world, in which case nothing science can get right would conflict with a belief in God and belief in God cannot conflict with science.

I think you've got a habit of switching around the meanings of words in order to press an ideological agenda, calling what most people call "belief" "knowledge" because it allows you to pretend to knock over what they believe on the basis of it not standing up to scientific standards of verification. Only, that's a dangerous game because sometimes what scientists assert they know, they really believe. And there is no better example of that than Richard Dawkins and his myriad of atheist admirers.

Nobody 'fully understands' evolution, Larry. You are sounding decidedly religious when you write something like that, as if you possess some arcane wisdom that only a select few are privy to.

And yet at least three ironies arise from that. 1.) It is not possible to 'fully understand' evolution until it is understood how life came to be in the first place. You might as well try to understand an automobile without understanding movement.2.) Evolution has been studied by so many people for so many years, that, collectively, you have no doubt reached a 'genius level' of understanding about its mechanisms. Evolution has been observed by more smart people than perhaps any other subject in the world. And yet no one has been able to conduct an experiment that brings this apparently blind, unguided process into being. No high school kids in a garage, and no consortium of PhDs in a lab. They can put a man on the moon, but they can't do something that nature didn't even realize it WAS doing, even after all those millions of hours spent studying.3.) It seems rather odd, doesn't it, that something that came about completely blindly, completely oblivious to itself, should nevertheless be so difficult to understand that only a few people really 'get it'? What's so hard to understand? How can a process be so 'dumb', and at the same time so nettlesome that it manages to fool even people who spend years studying it?

If you are entirely convinced of the truth of evolution then you can't be a creationist.

I accept that evolution is a fact, that it is true and, by your definition, I'd be a creationist. I wouldn't call myself one because I don't believe the creation story in Genesis is an actual account of how organisms came about. Though, as I pointed out here earlier, Theodosius Dobzhansky said:

It is wrong to hold creation and evolution as mutually exclusive alternatives. I am a creationist and an evolutionist.

Larry Moran, do you think he wasn't "entirely convinced" of the truth of evolution? You're certainly familiar with that short essay he said that in, the one that is famously titled:

Even more surprising was Koonin’s recent interpretation of the Central Dogma in a recent article entitled Does the central dogma still stand? , which I think is completely mistaken. What to you make of it?

Why are there so many well published scientists who misunderstand this basic concept?

Koonin understands perfectly well what the Central Dogma of Molecular Biology means. His paper is about possible transfers of information from protein back to nucleic acid. That WOULD BE a violation of the Central Dogma.

I'm going to post an article about Koonin's view. Thanks for the link.

Shapiro substitutes microorganisms for God as his teleological agent of what (just to confuse things further and piss everyone off) I'll call "designed evolution." Shapiro believes microorganisms can choose their own mutational pathways, which leads him to similar conclusions regarding "junk" DNA as the Intelligent Design folks - it's a vast reservoir of future-looking resources! (Compare the Intelligent Design doctrine of "front-loading.")

However, after more research, even the co-authors of Shapiro's early papers on this so-called "directed mutation" have backed away from thinking there's teleology involved. They've encountered too many situations where there are obviously beneficial mutational pathways that microorganisms are *not* taking for very, very long spans of generational time (e.g., Richard Lenski's wonderfully careful experiments). What's come out of this research is interesting stuff on mutation *rate* in microorganisms speeding up under various kinds of stress, but no evidence whatever that the little buggers are able to choose favorable mutational paths.

I think the fact that a theory so vague, so insufficiently verifiable and so far from the criteria otherwise applied in “hard” science, has become a dogma, can only be explained on sociological grounds. Society and science have been so steeped in the ideas of mechanism utilitarianism, and the economic concept of free competition, that instead of God, Selection was enthroned as ultimate reality.

Ludwig von Bertalanffy 1969: Perspectives on General System Theory, as famously quoted by Stephen Jay Gould

If people do or don't see teleology seems to be dependent on whether they want to see it or want not to see it. Or, maybe, if they're open to seeing it and closed to seeing it. I wonder if Darwin had thought there was more to be gained by siding with Gray instead of Haeckel and Vogt if he'd have leaned that way. Either way, science can't see it.

Jud: What's come out of this research is interesting stuff on mutation *rate* in microorganisms speeding up under various kinds of stress, but no evidence whatever that the little buggers are able to choose favorable mutational paths

I just want to point out that the “little buggers” might not be able to choose favorable mutations, but they might be able to choose in which genes they are going to increase the rate of mutations in order to speed up adaptation, so in that sense they can “choose favorable mutational paths.”

You have proposed a hypothesis. What I was talking about were the peer-reviewed published experimental results. If you look at more recent work by folks such as Cairns, Barry G. Hall, and others you will see a backing away from any suggestions of a mechanism, whether you call it directed mutation or directed transcription, by which microorganisms non-randomly choose mutational pathways.

I already told you that such "mechanism for adaptive mutagenesis" was shown not to be so. That microorganisms do not choose which genes will suffer mutations at all. Look for articles by John Roth in PNAS.

Jud: You have proposed a hypothesis. What I was talking about were the peer-reviewed published experimental results

Negative Entropy: I already told you that such "mechanism for adaptive mutagenesis" was shown not to be so

You might want to take a look at this peer-reviewed published experimental results in a reputable journal, Journal of Bacteriology (you might not be aware, but a ‘peer-reviewed paper’ doesn’t mean anything these days, because with a few hundred bucks you can publish basically anything you want in hundreds of peer reviewed journals):

Abstract Adaptive (stationary phase) mutagenesis is a phenomenon by which nondividing cells acquire beneficial mutations as a response to stress. Although the generation of adaptive mutations is essentially stochastic, genetic factors are involved in this phenomenon. We examined how defects in a transcriptional factor, previously reported to alter the acquisition of adaptive mutations, affected mutation levels in a gene under selection. The acquisition of mutations was directly correlated to the level of transcription of a defective leuC allele placed under selection. To further examine the correlation between transcription and adaptive mutation, we placed a point-mutated allele, leuC427, under the control of an inducible promoter and assayed the level of reversion to leucine prototrophy under conditions of leucine starvation. Our results demonstrate that the level of Leu(+) reversions increased significantly in parallel with the induced increase in transcription levels. This mutagenic response was not observed under conditions of exponential growth. Since transcription is a ubiquitous biological process, transcription-associated mutagenesis may influence evolutionary processes in all organisms.

Read carefully and you will notice that "adaptive mutations" in the abstract itself are not defined as directed to the necessary genes, but as being essentially a random process. They redefined the terms. These are no longer the "adaptive mutations" that Cairns was claiming, but rather the random mutational load that Roth et al. discovered and carefully demonstrated.

Having a higher mutational rate does not mean the same as having a mutation directed against a necessary gene. Does it?

Negative Entropy: These are no longer the "adaptive mutations" that Cairns was claiming, but rather the random mutational load that Roth et al. discovered and carefully demonstrated

In the Abstract, the authors say that in their study, the "adaptive mutations" in the specific gene (leuC) that they placed under selection were generated by a transcription-based mechanism as I suggested:

The acquisition of mutations was directly correlated to the level of transcription of a defective leuC allele placed under selection.

Some additional excerpts from the text of the paper that say the same thing:

These experiments clearly demonstrate an influence of transcription on the adaptive mutation phenomenon.

In this study, we have demonstrated the association of transcription with mutation in an inducible allele in stationary cells under selective pressure. Such an association could explain why adaptive mutations often appear directed and how cells under these conditions avoid the accumulation of lethal mutations resulting in genetic load, thus resolving this biological conundrum.

Although the generation of adaptive mutations is essentially stochastic

Stochastic. See? Not directed. They used that gene as a marker, and this is what they mean when they mention the gene and its level of transcription, and such stuff. That does not mean that the process was directed. They do try and show that there is a bias in such mutagenesis. Yet again, not a directed mutagenesis, but one that correlates with the levels of transcription. Far from the directed that Cairns was talking about.

The wording is a tad confusing if you don;t pay enough attention, and if you are still under the influence of Cairns articles. But if you pay enough attention they are not claiming directed mutations to the place and gene in need, but one where a bias seems to exist probably associated to levels of transcription, which makes some sense.

The generation of mutations in the gene under selection, in the case of this study, leuC, is indeed random. However, that’s not the point of my hypothesis, nor that of this paper.

The point is that an increase of the transcription rate in leuC by the selective agent only increases its rate of mutation, not that of other genes. Therefore, the increase rate of mutation in this case is specific for leuC, not for other genes. And, an increase in the mutation rate of leuC will generate more genetic variation at this locus (not at other loci), both in the individual and in the population, which will speed up the adaptation process at this locus.

Maybe, we need some other people to clarify this issue, and I think Larry might be willing to help with this. What do you think, Larry?

Nope, any expressed genes suffered mutations according to their level of expression. It only happens that these researchers investigated the issue by mutating that gene so that they could follow that gene as an example about how "adaptive mutations" happen. Again, not directed. Thus, the apparent direction you see in the discussion is due to two features of the experimental design: they mutated and followed only this gene, and they controlled the expression of this gene to measure the relationship between expression and mutation rate.

It is very important to check these things carefully before allowing yourself to jump into confirmation bias and thus wrong conclusions. As I said. It is already demonstrated that mutations occur all over the place. Only we get to see the ones who happened to grow because they reverted their auxotrophy.

Negative Entropy: Nope, any expressed genes suffered mutations according to their level of expression

Yes, that’s correct. That’s the point of my hypothesis and their study: the rate of mutation is directly associated the rate of transcription (i.e. expression).

That means that there is more genetic variation produced in genes that are highly transcribed compared to those that are silent or transcribed at low levels, and hence a differential rate of evolution.

According to your hypothesis, genes that are not transcribed at all in the germ line in animals—and there are lots of these genes—should have much shorter phylogenetic trees than those that are transcribed in the germ line. There's no evidence of such a difference that I know of.

Look at the globin genes, for example. Their mutation rate should be much lower than that of genes for the standard metabolic pathways. I don't think this is observed.

You raised a very interesting point/observation, and I’m not aware of any evidence, either. It should be an interesting project: compare the length of phylogenetic branches of the genes that are expressed at high level in the germ line vs those that are not.

However, this study needs to be done very carefully because of the variable rate of selection at different loci. In this study, the focus should be on sequences that are not under selective pressure, such as intron regions that are not involved in regulatory functions, or at nucleotide positions that allow synonymous mutations.

Maybe, Joe Felsenstein might want to take a look at this!

Back to the paper in discussion here, do you think it is valid? I mean, was the rate of mutation directly associated the rate of transcription in their study?

I would like to make it clear that the term “adaptive mutagenesis” as used in my hypothesis and in the discussion above is a misnomer.

However, it appears that, under certain environmental or experimental conditions, the rate of generating mutations, which are random or arbitrary in nature, in the genes that are highly transcribed (i.e. expressed) is higher than in the genes that are silent or have a low rate of transcription.

An increase in the number of random mutations in a highly transcribed gene leads to an increase in genetic variation at that locus, both at the individual and population levels, which can lead to a differential rate of evolution.

Theoretically, testing for this hypothesis is relatively straightforward; count the number of mutations in DNA sequences that are highly transcribed versus those that are not. However, because the number of mutations is relatively low, detecting them directly, such as by DNA sequencing, is a rather difficult task, although possible. For that reason, previous studies used indirect approaches, such as counting the number of organisms in a population that undergo a phenotypic change indicative of specific nucleotide substitution. The underlying presumption is that this selected nucleotide substitution accurately reflexes the rate of mutation.

As discussed in the previous comments, an alternative approach would be to investigate the number of nucleotide substitutions (or other types of mutations) over many generations, in DNA sequences that are differentially transcribed and, preferably, have not been under purifying or positive selection; in these cases, genetic drift notwithstanding, the rate of fixation represents more or less the rate of mutation.

The advantage of this approach is that it is a relatively direct account of the rate of mutation, and that it can be used for complex organisms, such as humans. In humans, for example, the study would involve a comparison between DNA sequences that are transcribed at different rates in the germ line and are not under strong positive or purifying constrains. And, the best part about this study is that the raw data is already there, in the GenBank, ready to be plugged in an analysis program. Anyone?

Larry - you seem so sure of yourself and "the truth of evolution." But that's what I'm talking about. The way I see it, there are two types of proponents of Darwinian evolution. The type that respects opposing views and the type that doesn't. I have a great amount of respect for the former type, but you are not in that group. You are not willing to give your opponents their due - basic respect. You only have to look to Charles Darwin to see what basic respect looks like.

"I am quite conscious that my speculations run quite beyond the bounds of true science," he said in a letter to Asa Gray.

In another letter to a colleague about Origin of Species, he had this to say: "...it will be grievously too hypothetical. It will very likely be of no other service than collocating some facts...alas, how frequent, how almost universal it is in an author to persuade himself of the truth of his own dogmas."

Even in the Origin of Species, his humility and respect for opposing views shows through: "I am well aware that scarcely a single point is discussed in this volume on which facts cannot be adduced, often apparently leading to conclusions directly opposite to those at which I have arrived. A fair result can be obtained only by fully stating and balancing the facts and arguments on both sides of each question..."

The moment you start looking at the scientific arguments and empirical evidence of intelligent design without that lazy, knee-jerk label "creationist", your respect-o-meter will spike and you'll be a better man for it. Remember, you must be able to separate (whether you like it or not!) a scientific theory from its implications. It's what James Shapiro is doing, and I respect him for it.

The way I see it, there are two types of proponents of Darwinian evolution.

I am not a proponent of "Darwinian evolution."

You do not respect evolutionary biologists enough to even identify them correctly. Why do you think you deserve to be respected for your ignorance and your insults?

The moment you start looking at the scientific arguments and empirical evidence of intelligent design without that lazy, knee-jerk label "creationist", your respect-o-meter will spike and you'll be a better man for it.

Please read the Wikipedia article on creationism. Then come back here and apologize for being so ignorant. Show some respect for people who are using the word "creationist" in a perfectly standard way even though you choose a different meaning.

Wikipedia may not be the standard for knowledge and truth but it serves very nicely as a standard for what a lot of people might think. Clearly there are quite a few people out there who use the word "creationist" exactly as I do.

I think you should show a bit or respect for people who disagree with you instead of implying that they use a "lazy, knee-jerk label" that just happens to be identical to one used all over the world.

Explain how an evolutionary biologist is not a proponent of Darwinian evolution.

Read: Why I'm Not a Darwinist. This is a well-known criticism of how the creationists describe scientists. We all know why they prefer to call us Darwinists and it has nothing to do with accuracy or respect.

The fact that you aren't familiar with the problem suggests that you haven't done your homework. It also suggests that you are so out of touch with evolutionary biology that you don't even recognize an insult when you use it.

What "scientific arguments and empirical evidence of intelligent design"? Intelligent Design has had more than twenty years to present both, but no peer-reviewed scientific papers of original research in any of the major tenets of Intelligent Design creationism have ever been published in journals like Nature, Science, Evolution, Microbe, American Naturalist, etc. Instead, like the notorious Intelligent Design creationist David Klinghoffer, "Design Theorists" - to use Klinghoffer's colleague William Dembski's term - have engaged in ignoring evidence contrary to their claims, grossly distorted published scientific research as "proof" for their views, and have even engaged in lies like Klinghoffer's morally repugnant Darwin = Hitler + Holocaust meme. (All of which, I might add, James Shapiro has been doing, since his most recent papers of published original research were with Rick (von) Sternberg.)

Intelligent Design IS creationism. Long before Judge Jones issued his Kitzmiller vs. Dover ruling, eminent philosophers of science like Robert Pennock were recognizing this; in Pennock's case, his definitive "deconstruction" of creationism, "Tower of Babel", which explains how and why Intelligent Design should be seen as a "flavor" of creationism. Intelligent Design is also recognized as a religiously motivated, pseudoscientific intellectual scam heavily promoted by ulta right-wing organizations and individuals like the Discovery Institute - the employer of Dembski, Klinghoffer and Sternberg BTW - and Howard Ahmanson (a major Discovery Institute donor) as described extensively in philosopher Barbara Forrest (who discussed the "evolution" of "Of Pandas and People" as a key plaintiff witness during the Kitzmiller vs. Dover trial) and biologist Paul R. Gross in their superb "Creationism's Trojan Horse: The Wedge of Intelligent Design.

Since no credible scientific research has ever been published in peer-reviewed scientific journals, but instead, promoted as the mendacious intellectual pornography that it is courtesy of Dembski, Klinghoffer and their fellow delusional Discovery Institute Intelligent Design creationists, then Intelligent Design is not science, but creationism, PERIOD.

@John: Uh, oh...there's the dreaded word "period" in ALL CAPS. That must certainly mean there's no argument and we can all go home.

And there are all the tired keywords we've all heard applied to ID before - "delusional", "pseudoscientific", "scam", "religiously motivated", and the like.

If you look back at all major scientific revolutions, proponents of the new idea are always vilified, mocked, and cold-shouldered. A sure sign we're on to something. And if you are not willing to be open to seeing things differently, then you'll eventually be consigned to history as those that made the loudest noise when the scientific revolution came around.

@Larry - Wikipedia serves nicely as a standard for what a lot of left-wing volunteer editors with too much time on their hands might think. If a person tries to amend their errors and lies, they'll change it right back within minutes instead of actually looking into it and searching for the truth.

I would like to respect you, Larry, I really would. But you'd have to meet me half way. You don't show an ounce of respect for the science of intelligent design. You are blinded by the uncomfortable implications of the theory.

Didn't like the "lazy, knee-jerk label" language I used? Well, think about it. You might not think it is lazy or knee-jerk now because you've used the term "intelligent design creationist" for so long. But back when you first started using it, I'm betting it was knee-jerk then. Sometimes we can't see past our worldview, even when we are staring at evidence that would tell us something else.

So, you don't like the term "Darwinist" because you think it's too narrow a definition. Perhaps. It was Huxley who coined it to refer to Charles Darwin's theory of evolution by natural selection acting on random mutations. I used the term "proponent of Darwinian evolution" which isn't the same thing as "Darwinist". You prefer "evolutionary biologist" to take into account the modern evolutionary synthesis. Understandable. Well, if you want others to use your preferred term because you think it explains your position better, why not offer the same courtesy to proponents of intelligent design theory?

ID is nothing but an argument from incredulity. The premise is, that the advocates can't understand how certain biological structures could have evolved from less complicated antecedents (e.g. the bacterium flagellum), therefore it must have been intelligently designed. This is nothing more then a restatement of Paley's watch analogy.

Larry - admitting something is the first step to changing it. You admit you "don't have an ounce of respect for intelligent design creationism", as you continue to label it. Good, well at least that's official, even if it has been obvious.

Now, I'm challenging you to change. Do you want your blog to be an exercise in preaching to the choir? That's too easy. Toss in some respect for those who oppose your ideas and a little time to look objectively at the evidence for intelligent design in biology and cosmology, and you just might have a blog that's worth reading.

By definition, "creationism is the religious belief that humanity, life, the Earth, and the universe are the creation of a supernatural being [...]". So no matter if you believe in evolution as a process, if you also believe in a god, and consider him the creator of life and (presumably) the architect of evolution, you are by very definition 'a creationist'.

Shapiro's book, the cover of which you show above, appeared in the iTunes bookstore a while back - I downloaded the free sample. I just finished the first chapter and a half or so. It's weird - sound science mixed with straw men, non sequiturs, weak analogies and bizarre use of language (DNA formatting??). It's almost as though he wanted to use computer analogies to explain the science, and then forgot that it was just an analogy. He talks about "cognitive processes' as though cells are thinking about what they are doing when they correct replication errors. Read/write systems?? Shapiro has gone off the reservation with this book - it's no surprise he consorts with ID creationists.

Shpaior most certainly has "gone off the reservation" with his book. I haven't read it, but have been following his blogs - as well as commenting there - and would recommend skipping his book. What he has been advocating in his book, his Huffington Post blogs, and other articles for most of the last decade and a half is his unique, quite weird, "Third Way" Neo-Lamarckian evolutionary theory which operates via "Natural Genetic Engineering" and the "cognitive behavior" of cells. He claims his "National Genetic Engineering" does support the existence of "irreducibly complex" biological structures and functions - a central tenet of Intelligent Design "theory" - but the problem with his inane claim is that "irreducible complexity" has been rejected by many credible scientists ever since Intelligent Design creationist Michael Behe proposed it in his book "Darwin's Black Box". Shapiro's Intelligent Design creationist admirers appreciate his "recognition" of "irreducible complexity" and in providing for his readers, a "strawman" version of current evolutionary theory and current evolutionary biology virtually indistinguishable from Intelligent Design creationist "gospel".

I am in full agreement, Sam Harris. But he's been doing this for months. I urge those who find objectionable, Shapiro's polemical monologues masquerading as blogs to complain directly to Huffington Post. I've told them that Shapiro is performing a great disservice to his colleagues, grossly distorting and misinterpreting published science to fit with his heterodox views, greatly damaging public understanding of science. He is also a serious obstacle towards Huffington Post Science's goal of reporting only on good science. He should cease blogging there immediately for these reasons.

Laurence A. Moran

Larry Moran is a Professor Emeritus in the Department of Biochemistry at the University of Toronto. You can contact him by looking up his email address on the University of Toronto website.

Sandwalk

The Sandwalk is the path behind the home of Charles Darwin where he used to walk every day, thinking about science. You can see the path in the woods in the upper left-hand corner of this image.

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Some readers of this blog may be under the impression that my personal opinions represent the official position of Canada, the Province of Ontario, the City of Toronto, the University of Toronto, the Faculty of Medicine, or the Department of Biochemistry. All of these institutions, plus every single one of my colleagues, students, friends, and relatives, want you to know that I do not speak for them. You should also know that they don't speak for me.

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Quotations

The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Quotations

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake.
Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.
Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change.
Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance.
Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change.
Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.
Stephen Jay Gould (1999) p.84

Quotations

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is TrueI once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000
It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma
One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick
There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner
An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins
Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod
The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.